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  • Merge Assemblies with Cuffmerge Element
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Cuffmerge merges together several assemblies. It also handles running Cuffcompare for you, and automatically filters a number of transfrags that are probably artifacts. If you have a reference file available, you can provide it to Cuffmerge in order to gracefully merge input (e.g. novel) isoforms and known isoforms and maximize overall assembly quality.

Parameters in GUI

ParameterDescriptionDefault value
Output directoryDirectory to save MACS output files. 
Reference annotationMerge the input assemblies together with this reference annotation. 
Reference sequenceThe genomic DNA sequences for the reference. It is used to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, transcripts consisting mostly of lower-case bases are classified as repeats. 
Minimum isoform fractionDiscard isoforms with abundance below this.0.05
Cuffcompare tool pathThe path to the Cuffcompare external tool in UGENE.default
Cuffmerge tool pathThe path to the Cuffmerge external tool in UGENE.default
Temporary directoryThe directory for temporary files.default

Parameters in Workflow File

Type: cuffmerge

ParameterParameter in the GUIType
out-dirOutput directory


ref-annotationReference annotationstring
ref-seqReference sequencestring
min-isoform-fractionMinimum isoform fractionnumeric
cuffcompare-tool-pathCuffcompare tool pathstring
pathCuffmerge tool pathstring
tmp-dirTemporary directorystring

Input/Output Ports

The element has 1 input port:

Name in GUI: Set of annotations

Name in Workflow File: in-assembly


Slot In GUISlot in Workflow FileType
Set of annotationsin-annotationsann_table

And 1 output port:

Name in GUI: Set of annotations

Name in Workflow File: out-assembly


Slot In GUISlot in Workflow FileType
Set of annotationsout-annotationsann_table
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